Sequence
atgc intronic sequence ATGC exonic sequencegtatggctttcatcaatagatgaattattttagcaattcatgaagtcctactaatcagttttttatttttggtgaaaattttagATGAGTGGTTCAAGAATGAAGATTGCTGGAAGATTTAAACCCTGTATTCACATGGGTTGCTTTGATCTTGAAGTGTTTGTGGAAATGAACCAACGATCAA
Basic information
species | Glycine max |
transcript | GLYMA12G07590.1 |
intron # | 13 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA12G07590.1 (Glycine max), 3'ss of exon 13
lower sequence: LOC_Os05g03430.3 (Oryza sativa), 3'ss of exon 8
-------------------gtatggctttcatcaatagatgaattattttagcaattcatgaagtcctactaatcagttttttatttttggtgaaaattttagATGAGTGGTTCAAGAATGAAGATTGCTGGAAGATTTAAACCCTGTATTCACATGGGTTGCTTTGATCTTGAAGTGTTTGTGGAAATGAACCAACGATCAA
|| | | | || | | | || | | || || | ||||||| | ||| |||| | || ||| ||||| || ||||||| ||||||||| ||||| || || || |||||||||||||| |||||||||||| || |||||| |||| ||||| ||
atataggttctaatgtcatgtcaagatgtgtgtaa-ggctaagcctttcttgtgatgcaaaattggagactaatc--taatttgttttctaacatgtcttcagAATAGTGGATCCAGAATGAGGATTGCTGGGAGATTCAAGCCTTGCATTCACATGGGTTGTTTTGATCTTGAAACTTTCGTGGAATTGAATCAACGGTCCC
upper sequence: GLYMA12G07590.1 (Glycine max), 3'ss of exon 13
lower sequence: LOC_Os03g50980.1 (Oryza sativa), 3'ss of exon 12
--------gtatggctttcatcaatagatgaattattttagcaattcatgaagtcctactaatcagttttttatttttggtgaaaat----ttta--------gATGAGTGGTTCAAGAATGAAGATTGCTGGAAGATTTAAACCCTGTATTCACATGGGTTGCTTTGATCTTGAAGTGTTTGTGGAAATGAACCAACGATCAA
|||||||| || | | ||| | | ||||| || | | | ||||| | || | | | || | | ||||||| |||| ||||| ||||||||| || ||||| ||||| | || |||||||| ||||||||||||| |||||| | |||| ||||||||| | || ||||| ||||
tattcatagtatggctgacactacttcatgca--aagttagctatgaa-gtactccta-tgatatctgtataatgtctcatgaaaatgccttttatcttgacagATGACTGGTTCAAGGATCAAGATAGCTGGCCGGTTCAAACCCTGCGTTCACATGGGTTGTTTTGATTTAGAAGCTTTTGTGGAACTTAATCAACGTTCAA
upper sequence: GLYMA12G07590.1 (Glycine max), 3'ss of exon 13
lower sequence: GRMZM2G155123_T02 (Zea mays), 3'ss of exon 12
--------------------gtatggctttcatcaatagatgaattattttagcaattcatgaagtcctactaatcagttttttatttttggtgaaaattttagATGAGTGGTTCAAGAATGAAGATTGCTGGAAGATTTAAACCCTGTATTCACATGGGTTGCTTTGATCTTGAAGTGTTTGTGGAAATGAACCAACGATCAA
||| ||| |||| ||| | | | | | || | | | | | | ||||||| | ||| ||| || || || ||||||| |||||||||||| || || || ||| |||||||||| || |||||||||||| ||||||||| |||| ||||| |||
agcatatcttttctggttggctatagctgtcatgtttagctaagctgctccggtgcaatttgcatttggaattgtatctaacatattttttatt----tttcagAATAGCGGATCCAGAATGAGGATTGCTGGAAGGTTCAAGCCTTGTGTTCACATGGGCTGTTTTGATCTTGAAACTTTTGTGGAATTGAATCAACGCTCAC
upper sequence: GLYMA12G07590.1 (Glycine max), 3'ss of exon 13
lower sequence: AT5G60410.4 (Arabidopsis thaliana), 3'ss of exon 13
---------------------gtatggctttcatcaatagatgaattattttagcaattcatgaagtcctactaatcagttttttatttttggtgaaaattttagATGAGTGGTTCAAGAATGAAGATTGCTGGAAGATTTAAACCCTGTATTCACATGGGTTGCTTTGATCTTGAAGTGTTTGTGGAAATGAACCAACGATCAA
| | ||| || | | || | || || | | | | || | ||| || | ||||||||| ||||| || || || ||||||| |||||| ||||||| | |||||||| || ||||| ||||| ||||||||||| |||| ||||| || |
gtaagttactaatagctcgtagcccagtttttat-acttatcctcttcctagggctatcttgcagactgaattttttttattgtcttttctgtttgcgtcattagATGAGCGGTTCTAGGATAAAAGTTGCTGGGAGATTTTTACCCTGTGTGCACATGGGCTGTTTTGACCTTGATGTGTTTGTGGAGTTGAATCAACGTTCCA
upper sequence: GLYMA12G07590.1 (Glycine max), 3'ss of exon 13
lower sequence: Vv06s0004g03180.t01 (Vitis vinifera), 3'ss of exon 12
-gtatggctttcatcaatagatgaattattttagcaat----tcatgaagtcctactaatc----agttttttatttttg-------gtgaaaattttagATGAGTGGTTCAAGAATGAAGATTGCTGGAAGATTTAAACCCTGTATTCACATGGGTTGCTTTGATCTTGAAGTGTTTGTGGAAATGAACCAACGATCAA
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gtttttgatgcagaaaacccaataacttttgttgcaatgcttttatgtaacctgattacttttggaatcatatatttttactcatacatgtaaattacagATGAGTGGTTCAAGAATGAAGGTTGCTGGAAGATTCAAACCTTGTGCTCACATGGGCTGTTTTGATCTTGAAATTTTTGTGGAAATGAACCAACGTTCTAMapped EST sequences
Showing partial alignments of ESTs and genomic sequences. See full alignments
ATGC EST sequence
ATGC genomic sequence (exon)
ATGC genomic sequence (truncated intron)
EST:
gi|23729846|gb|BU763027.1|BU763027EST: GTGATTTGGAAGTGGTTTCAGATACTTTCACTGTCAACCTTCGTTGTCCT ATGAGTGGTTCAAGAATGAAGATTGCTGGAAGATTTAAACCCTGTATTCAC
genomic: GTGATTTGGAAGTGGTTTCAGATACTTTCACTGTCAACCTTCGTTGTCCTgtatggcttt ... aaaattttagATGAGTGGTTCAAGAATGAAGATTGCTGGAAGATTTAAACCCTGTATTCAC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttagcaattcatgaagtcctactaatcagttttttatttttggtgaaaattttagATGAGTGGTTCAAGAATGAAGATTGCTGGAAGATTTAAACCCTGTATTCACATGGGTTGCTTTGATCTTGAAGTGTTTGTGGAAATGAACCAACGATCAA
tactaat putative branch site (score: 1)
agttttttatttttgg TA-rich tract
Putative cis-regulatory sequences
atgc | intron | ATGC | exonic elements by Pertea et al. |
ATGC | exon | atgc | putative intronic elements |
| | ATGC | putative exonic elements identified for retained introns |
10 20 30 40 50 60 70 80 90 100 110 120 130 140 150 160 170 180 190 200 210 220
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatggctttcatcaatagatgaattattttagcaattcatgaagtcctactaatcagttttttatttttggtgaaaattttagATGAGTGGTTCAAGAATGAAGATTGCTGGAAGATTTAAACCCTGTATTCACATGGGTTGCTTTGATCTTGAAGTGTTTGTGGAAATGAACCAACGATCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG